Contacts of the helix formed by residues 41 - 58 (chain A) in PDB entry 3QOQ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 41 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ARG* 1.3 79.6 - - - +
42A MSE 1.3 60.0 + - - +
43A ASN* 3.8 0.9 + - - +
44A SER* 3.0 15.1 + - - -
45A GLU* 2.9 24.9 + - - +
11E C 2.6 48.4 + - - -
12E G 3.8 10.8 - - - -
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Residues in contact with MSE 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 6.0 1.1 - - - -
28A ARG* 4.2 37.7 - - - +
31A ILE* 3.4 29.2 - - + -
32A ALA* 4.4 19.3 - - + -
35A ALA* 4.4 7.7 - - + +
41A SER* 1.3 69.0 - - - +
43A ASN* 1.3 66.6 - - - +
45A GLU* 3.2 5.4 + - - +
46A ILE* 3.0 30.4 + - + +
19B PHE* 3.7 31.4 - - + -
12E G 2.9 28.0 + - - +
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Residues in contact with ASN 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A SER* 3.2 1.8 - - - +
42A MSE 1.3 78.9 - - - +
44A SER* 1.3 62.9 + - - +
46A ILE* 3.1 3.8 + - - +
47A ILE* 3.0 35.8 + - - +
19B PHE* 3.8 9.8 - - + -
20B VAL 4.5 3.3 - - - +
21B VAL* 4.0 6.4 - - - +
22B ARG* 2.8 57.8 + - - +
11E C 3.9 24.5 + - - +
12E G 3.0 16.9 + - - +
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Residues in contact with SER 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ARG* 3.7 8.2 - - - -
41A SER* 3.0 12.9 + - - -
43A ASN* 1.3 77.9 - - - +
45A GLU* 1.3 57.1 + - - +
47A ILE* 3.7 8.4 - - - +
48A ALA* 2.8 33.6 + - - +
39C HIS* 3.3 36.1 + - - +
40C ARG* 5.6 0.2 - - - -
11E C 2.8 25.1 + - - -
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Residues in contact with GLU 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ILE* 4.1 16.8 - - + +
34A VAL* 3.6 8.0 - - + +
35A ALA* 3.2 37.7 + - + +
38A HIS* 3.9 0.5 - - - +
40A ARG* 3.1 34.4 + - - +
41A SER 2.9 14.7 + - - +
42A MSE 3.3 10.1 - - - +
43A ASN 3.1 0.2 - - - -
44A SER* 1.3 78.2 - - - +
46A ILE* 1.3 64.2 + - - +
48A ALA* 3.2 0.9 + - - +
49A ARG* 2.5 64.6 + - - +
54B LEU* 6.4 0.2 - - + -
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Residues in contact with ILE 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A VAL* 5.6 5.8 - - + -
23A LEU* 5.8 6.7 - - + -
31A ILE* 3.9 24.2 - - + -
42A MSE 3.0 18.0 + - + +
43A ASN 3.5 4.5 - - - +
45A GLU* 1.3 73.0 - - - +
47A ILE* 1.3 64.4 + - - +
49A ARG* 3.2 8.0 + - - +
50A LEU* 2.9 41.5 + - + +
19B PHE* 4.2 20.9 - - + -
21B VAL* 4.2 21.5 - - + -
46B ILE* 4.9 5.4 - - + -
50B LEU* 3.7 31.8 - - + +
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Residues in contact with ILE 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ASN* 3.0 30.9 + - - +
44A SER* 3.7 7.2 - - - +
46A ILE* 1.3 74.2 - - - +
48A ALA* 1.3 59.1 + - - +
50A LEU* 3.2 3.5 + - + -
51A GLU* 2.8 33.1 + - - +
21B VAL* 3.8 7.6 - - + -
22B ARG 3.4 20.4 - - - +
23B LEU* 3.7 18.2 - - + -
24B PRO* 3.6 27.8 - - + -
27B MSE 3.5 18.4 - - + +
39C HIS* 3.7 25.8 - - + +
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Residues in contact with ALA 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ARG* 4.1 25.6 - - - +
44A SER 2.8 21.5 + - - +
45A GLU 3.2 4.2 + - - +
47A ILE* 1.3 72.9 - - - +
49A ARG* 1.3 61.4 + - + +
51A GLU* 3.7 4.7 + - - +
52A GLN* 3.1 23.9 + - - +
39C HIS* 3.7 28.0 - - + -
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Residues in contact with ARG 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ILE* 5.5 0.2 - - - -
34A VAL* 3.0 25.8 - - - +
38A HIS* 5.2 3.0 + - - -
40A ARG* 4.7 2.0 - - - +
45A GLU* 2.5 56.6 + - - +
46A ILE* 3.7 4.5 - - - +
48A ALA* 1.3 74.5 - - + +
50A LEU* 1.3 60.4 + - - +
52A GLN* 3.3 5.9 + - - +
53A SER* 2.9 30.9 + - - -
49B ARG* 6.2 0.7 - - - -
50B LEU* 4.2 24.2 - - + -
53B SER* 3.4 40.9 + - - +
54B LEU* 4.0 14.0 - - - +
57B GLU* 3.2 43.0 + - - +
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Residues in contact with LEU 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ILE* 2.9 37.6 + - + +
47A ILE* 3.6 2.7 - - - +
49A ARG* 1.3 74.3 - - - +
51A GLU* 1.3 54.7 + - - +
53A SER* 2.9 6.6 + - - -
54A LEU* 2.7 44.1 + - + +
21B VAL* 5.5 0.2 - - + -
23B LEU* 4.3 13.7 - - + -
27B MSE 4.1 22.2 - - - -
31B ILE* 4.3 15.0 - - + -
46B ILE* 4.0 26.2 - - + +
49B ARG* 4.1 19.1 - - + -
50B LEU* 3.6 22.2 - - + +
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Residues in contact with GLU 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ILE 2.8 22.6 + - - +
48A ALA 3.7 5.5 - - - +
50A LEU* 1.3 72.5 - - - +
52A GLN* 1.3 57.4 + - - +
54A LEU* 3.5 6.5 + - - +
55A LEU* 3.1 45.6 + - + +
27B MSE 3.4 19.6 - - + +
37C SER 4.9 3.6 - - - +
39C HIS* 3.1 32.3 + - - +
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Residues in contact with GLN 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ALA 3.1 14.5 + - - +
49A ARG* 3.7 4.3 - - - +
50A LEU 3.1 0.8 - - - -
51A GLU* 1.3 78.0 - - - +
53A SER* 1.3 64.3 + - - +
55A LEU* 3.3 9.1 + - + +
56A GLN* 3.1 50.8 + - + +
53B SER* 4.3 11.6 + - - -
56B GLN* 5.5 3.3 - - - +
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Residues in contact with SER 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ARG 2.9 17.5 + - - -
50A LEU 3.4 4.5 - - - -
52A GLN* 1.3 78.1 - - - +
54A LEU* 1.3 62.4 + - - +
56A GLN* 3.6 23.8 + - - +
57A GLU* 3.7 10.2 + - - +
49B ARG* 3.2 38.9 + - - +
52B GLN* 2.9 24.7 + - - -
53B SER* 4.6 6.7 + - - -
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Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LEU* 2.7 44.6 + - + +
51A GLU* 3.6 8.7 - - - +
53A SER* 1.3 73.1 - - - +
55A LEU* 1.3 63.8 + - + +
57A GLU* 3.2 16.3 + - + +
58A GLY* 3.3 8.8 + - - -
27B MSE 5.3 8.1 - - + -
30B GLN* 3.3 34.5 - - + +
31B ILE* 4.4 17.3 - - + -
34B VAL* 4.1 16.4 - - + -
49B ARG* 3.3 33.5 - - - +
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Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A GLU* 3.1 37.5 + - + +
52A GLN* 3.3 8.0 + - + +
54A LEU* 1.3 75.5 - - + +
56A GLN* 1.3 63.4 + - - +
58A GLY* 3.3 13.6 + - - +
59A ALA* 3.3 18.4 + - - +
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Residues in contact with GLN 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A GLN* 3.1 56.9 + - + +
53A SER* 3.7 14.8 - - - +
54A LEU 3.2 0.6 - - - -
55A LEU* 1.3 77.8 - - - +
57A GLU* 1.3 61.7 + - + +
58A GLY 3.5 0.3 + - - -
59A ALA* 3.6 15.3 + - - +
52B GLN* 4.2 12.7 + - - +
53B SER* 5.5 1.2 + - - -
56B GLN* 3.7 20.7 + - - +
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Residues in contact with GLU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A SER 3.7 8.9 + - - +
54A LEU* 3.2 9.1 + - - +
56A GLN* 1.3 77.2 - - + +
58A GLY* 1.3 60.5 + - - +
59A ALA 3.3 3.9 + - - +
34B VAL* 4.1 8.8 - - - +
38B HIS* 4.0 20.4 + - - -
49B ARG* 2.9 33.3 + - - -
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Residues in contact with GLY 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LEU 3.3 9.4 + - - -
55A LEU* 3.3 12.7 + - - -
57A GLU* 1.3 77.9 - - - +
59A ALA* 1.3 57.1 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il